When a gene is used to synthesize a protein, error checking and prevention is performed all along the way. An important and dangerous error is the so-called nonsense error in which the code for an amino acid is erroneously replaced with a stop signal. This causes the protein synthesis process to be halted in mid stream, leaving a half-baked and useless segment of protein. Cell’s have various processes to check for and correct such nonsense errors, but another way around the problem is to avoid the genetic coding that is particularly susceptible to nonsense errors.
The main contribution of Cusack’s paper is its elucidation of how these correction and prevention mechanisms often complement each other nicely. In particular, the error correction mechanisms have their limitations. One of the correction mechanisms usually doesn’t work for genes that are written out in one, single continuous region. And for genes that are divided into several separate regions, that mechanism often doesn’t work for the final region.
It is in these particular regions—where the error correction is more limited—that the prevention is stronger. In these regions, the particular genetic coding that is susceptible to nonsense errors is diminished. It would be like having a spell-checker that cannot check a certain page, but that page doesn’t have any long words to begin with.
This and other examples need nothing more than common sense to understand. Looking at the design of the error correction and prevention mechanisms, it makes perfect sense that where the error correction is less effective, there would be more error prevention. Nonetheless, the evolutionists break every rule of parsimony to impose their evolutionary framework. They multiply entities and construct superfluous causes. From Occam to Einstein we know not to do this, but evolutionists must have their theory. Here are two examples from the paper:
Given the high rate of transcriptional errors in eukaryotes, we hypothesized that natural selection has promoted a dual strategy of “prevention and cure” to alleviate the problem of nonsense transcriptional errors. A prediction of this hypothesis is that [the error correction’s] inefficiency should leave a signature of “transcriptional robustness” in human gene sequences that reduces the frequency of nonsense transcriptional errors.
Interestingly, one group of genes falls entirely outside of the range of [the error correction’s] surveillance. Replication-dependent histones contain neither introns in their coding sequences nor polyA-tail in their mRNAs. Therefore, histone genes represent a blind-spot for both mammalian [the error correction] pathways. According to our hypothesis histone genes should represent the most transcriptionally robust genes in the mammalian genome since PTC-containing transcripts of their genes will not be recognized and degraded before translation.
Evolution adds nothing to the science here. These are yet more examples of how evolution is a gratuitous explanation, adding nothing but “multiplied entities” as Occam put it. We may as well say, with the Aristotelians, that fire is hot because it has the quality of heat.
Evolution adds little to the science beyond gratuitous explanation, and furthermore that explanation is awkward. The theory states that the entire biological world just happened to arise all by itself.
Not surprisingly evolutionists never describe it this way. Nor do they use equally accurate but more detailed explanations, such as that blind mutations just happened to create complex, interdependent designs while natural selection killed off the bad designs. Such accurate explanations of the theory are not used because they make obvious the absurdity of the whole project.
Instead evolutionists craft clever explanations that cast evolution and its natural selection in the active role of a designer. The theory sounds so much more plausible when natural selection responds to a need by creating a new design. And so there is an underlying, latent Lamarckianism running through the evolution genre. Out of one side of their mouth they rail against teleology while from the other they appeal to it over and over. Here are typical examples from the paper:
we hypothesized that natural selection has promoted a dual strategy of “prevention and cure” to alleviate the problem of nonsense transcriptional errors.
Nonsense errors are potentially highly toxic for the cell, so natural selection has evolved a strategy called Nonsense Mediated Decay (NMD) to “cure” such errors.
Moreover, these “prevention and cure” strategies are used interchangeably …
Natural selection has promoted a dual strategy to alleviate a problem? Strategies are used interchangeably? Of course evolutionists do not mean any of this to be true. Their teleology is rhetorical. They need it to avoid the literal.
The evolutionists force-fit the evidence into their theory, and the fit isn’t very good. Cusack’s flawed thesis is that evolution predicts how the error correction and prevention methods complement each other. But as usual the project depends on the pre existence of biology’s wonders. In this case, the evolutionists believe that evolution just happened to create the genetic code, which conveniently just happened to have some stop signals.
Evolution also just happened to create genetic information, including stop signs at the appropriate places, and the incredible molecular machines to read, copy and translate that genetic information, and to stop at the stop signs.
But sometimes errors occurred which inserted stop signs somewhere in the middle of a copy of a gene. Fortunately, evolution just happened to create incredible molecular machinery and mechanisms to check for and correct for such errors. The likelihood of all (or any) of this happening is of course beyond ridiculous. The theory isn’t even wrong.
The only way to avoid evolution’s massive contradictions is simply to assume it is true. Having swallowed such lunacy the evolutionists are now in a position to declare that the new evidence is yet another fulfilled prediction of, yes, evolution. Evolution is true, therefore evolution is true.
Cum hoc ergo propter hoc
A common evolutionary fallacy is to confuse correlation with causation. In this case Cusack and the evolutionists find a good correlation between the correction and prevention mechanisms. Simply put, where the correction is weaker, the prevention is stronger. And so they assume the former is the cause of the latter via the evolutionary process:
We observe that single-exon genes have evolved to become robust to mistranscription, because they show a significant tendency to avoid fragile codons relative to robust codons when compared to multi-exon genes.
Depletion of fragile codons is due primarily to inactivity of EJC–dependent NMD but also to reduced efficiency of PABP–dependent NMD.
We show that variable NMD efficiency also leaves its signature in the coding sequences of human genes and in the amino-acid content of the proteins they encode.
When will evolutionists learn that correlation does not imply causation. The answer of course is that they will learn this only when they learn to stop corrupting science with their religious dogma. That may sound harsh, but that is precisely what evolutionists are doing. Their metaphysics mandates evolution to be true. Therefore such correlations must be assumed to be the result of evolutionary causation.
No evolutionary treatise would be complete without misrepresentations of the science. If there is any common thread to scientific evolutionism it is the very bizarre interpretations of the scientific evidence which, to put it kindly, amount to misrepresentations. Such misrepresentations run all though the genre, from the popular works on down to the technical papers. Consider these misrepresentations from Cusack’s paper:
In contrast, gene expression errors are not inherited and have tended to be disregarded in evolutionary studies. Here we show how human genes have evolved a mechanism to reduce the occurrence of a specific type of gene expression error—transcriptional errors that create premature STOP codons (so-called “nonsense errors”).
But of course the paper showed no such thing. It did not “show how human genes have evolved a mechanism …” That is an incredibly unlikely, religiously-driven hypothesis that makes little scientific sense. The paper continues:
Nonsense errors are potentially highly toxic for the cell, so natural selection has evolved a strategy called Nonsense Mediated Decay (NMD) to “cure” such errors. However this cure is inefficient. Here we describe how a preventative strategy of “transcriptional robustness” has evolved to decrease the frequency of nonsense errors.
These are yet more blatant misrepresentations of the science. The paper does not “describe how a preventative strategy of ‘transcriptional robustness’ has evolved to decrease the frequency of nonsense errors.” The paper not only did not describe how such a strategy evolved, it did not even show that it evolved.
Religion drives science, and it matters.